Variant report

Variant	rs12905062
Chromosome Location	chr15:76052162-76052163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76050716..76052261-chr15:76053754..76055876,2	K562	blood:
2	chr15:76038205..76040271-chr15:76051114..76054097,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC019294.2-1	chr15:76050881-76052477	ENSG00000260288.1

Variant related genes	Relation type
ENSG00000260815	Chromatin interaction
ENSG00000261043	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10163112	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10519109	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634290	0.92[JPT][hapmap]
rs11636280	0.82[JPT][hapmap]
rs11852472	0.82[ASN][1000 genomes]
rs11852712	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854305	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11858818	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898509	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899163	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12899303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900007	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900167	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904654	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905730	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13329104	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1823175	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1850261	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1964473	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1964474	0.88[ASN][1000 genomes]
rs1996302	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996303	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002668	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2004630	0.88[ASN][1000 genomes]
rs2004920	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009508	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010392	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2017312	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290484	0.95[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2405718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405719	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2405882	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28404806	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28541422	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615348	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28651447	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657001	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688252	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695212	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695716	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28744558	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28833005	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28837134	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243492	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34402412	0.85[EUR][1000 genomes]
rs34469290	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34571038	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34605750	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611707	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34909574	0.81[ASN][1000 genomes]
rs34941412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35019194	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35135316	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35136767	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35147271	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35237189	0.82[ASN][1000 genomes]
rs35411779	0.85[ASN][1000 genomes]
rs35575236	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35745834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35842909	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880865	0.82[ASN][1000 genomes]
rs36057011	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751536	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs3845233	0.88[ASN][1000 genomes]
rs3845234	0.88[ASN][1000 genomes]
rs3850092	0.89[ASN][1000 genomes]
rs3861184	0.91[ASN][1000 genomes]
rs4503758	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4616261	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs55744943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57905971	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60214227	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66838310	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs67908345	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71403504	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71403505	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71462532	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163633	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165531	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181595	0.81[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026532	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026234	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027311	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028002	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037672	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8041390	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8041670	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
3	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv974599	chr15:76033068-76101142	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76051200-76052200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:76051200-76052200	Enhancers	Stomach Mucosa	stomach
3	chr15:76051200-76052600	Weak transcription	Spleen	Spleen
4	chr15:76051400-76052200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:76051400-76052200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:76051400-76052200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:76051400-76052200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:76051400-76052200	Flanking Active TSS	Dnd41	blood
9	chr15:76051400-76052400	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:76051400-76052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:76051400-76052600	Weak transcription	Left Ventricle	heart
12	chr15:76051400-76053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:76051400-76054000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:76051400-76055600	Weak transcription	Pancreas	Pancrea
15	chr15:76051400-76057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:76051400-76059000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:76051400-76063200	Weak transcription	Right Atrium	heart
18	chr15:76051600-76052400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr15:76051600-76052400	Enhancers	Liver	Liver
20	chr15:76051600-76052400	Enhancers	Thymus	Thymus
21	chr15:76051600-76052400	Enhancers	HSMM	muscle
22	chr15:76051600-76052600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:76051600-76054600	Enhancers	Fetal Heart	heart
24	chr15:76051800-76052200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:76051800-76052200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:76051800-76052400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr15:76051800-76052400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:76051800-76052800	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:76051800-76053000	Weak transcription	Fetal Lung	lung
30	chr15:76051800-76053200	Weak transcription	HepG2	liver
31	chr15:76051800-76054800	Weak transcription	Fetal Brain Female	brain
32	chr15:76052000-76052200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr15:76052000-76052200	Flanking Active TSS	K562	blood
34	chr15:76052000-76052400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:76052000-76052400	Flanking Active TSS	GM12878-XiMat	blood
36	chr15:76052000-76052400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr15:76052000-76053600	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links